A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-11-25, 16:36 UTC
based on data in:
/gscratch/scrubbed/samwhite/gitrepos/ceasmallr/output/02.01-bismark-bowtie2-alignment-SLURM-array
General Statistics
| Sample Name | % Aligned | % Aligned |
|---|---|---|
| CF01-CM01-Zygote-1-bismark | 6.0% | |
| CF01-CM01-Zygote_R1_001 | 13.1% | |
| CF01-CM02-Larvae-2-bismark | 16.8% | |
| CF01-CM02-Larvae_R1_001 | 35.0% | |
| CF02-CM02-Zygote-3-bismark | 8.1% | |
| CF02-CM02-Zygote_R1_001 | 13.4% | |
| CF03-CM03-Zygote-4-bismark | 8.8% | |
| CF03-CM03-Zygote_R1_001 | 20.8% | |
| CF03-CM04-Larvae-5-bismark | 21.6% | |
| CF03-CM04-Larvae_R1_001 | 46.2% | |
| CF03-CM05-Larvae-6-bismark | 16.5% | |
| CF03-CM05-Larvae_R1_001 | 33.9% | |
| CF04-CM04-Zygote_R1_001 | 25.2% | |
| CF05-CM02-Larvae_R1_001 | 35.7% | |
| CF05-CM05-Zygote_R1_001 | 25.2% | |
| CF06-CM01-Zygote_R1_001 | 23.4% | |
| CF06-CM02-Larvae_R1_001 | 21.9% | |
| CF07-CM02-Zygote_R1_001 | 11.1% | |
| CF08-CM03-Zygote_R1_001 | 18.3% | |
| CF08-CM04-Larvae_R1_001 | 1.0% | |
| CF08-CM05-Larvae_R1_001 | 2.2% | |
| EF01-EM01-Zygote_R1_001 | 22.6% | |
| EF02-EM02-Zygote_R1_001 | 22.6% | |
| EF03-EM03-Zygote_R1_001 | 16.1% | |
| EF03-EM04-Larvae_R1_001 | 30.8% | |
| EF03-EM05-Larvae_R1_001 | 28.6% | |
| EF04-EM04-Zygote_R1_001 | 8.4% | |
| EF04-EM05-Larvae_R1_001 | 36.2% | |
| EF05-EM01-Larvae-23-bismark | 14.4% | |
| EF05-EM01-Larvae_R1_001 | 29.0% | |
| EF05-EM05-Zygote-24-bismark | 3.8% | |
| EF05-EM05-Zygote_R1_001 | 6.7% | |
| EF05-EM06-Larvae-25-bismark | 15.7% | |
| EF05-EM06-Larvae_R1_001 | 35.0% | |
| EF06-EM01-Larvae-26-bismark | 17.2% | |
| EF06-EM01-Larvae_R1_001 | 34.2% | |
| EF06-EM02-Larvae-27-bismark | 16.2% | |
| EF06-EM02-Larvae_R1_001 | 35.2% | |
| EF06-EM06-Larvae-28-bismark | 11.6% | |
| EF06-EM06-Larvae_R1_001 | 25.0% | |
| EF07-EM01-Zygote-7-bismark | 6.0% | |
| EF07-EM01-Zygote_R1_001 | 10.0% | |
| EF07-EM03-Larvae-8-bismark | 15.2% | |
| EF07-EM03-Larvae_R1_001 | 32.9% | |
| EF08-EM03-Larvae-9-bismark | 17.8% | |
| EF08-EM03-Larvae_R1_001 | 37.9% | |
| EF08-EM04-Larvae-10-bismark | 17.1% | |
| EF08-EM04-Larvae_R1_001 | 34.8% |
Bismark
0.24.2
Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167
Alignment Rates
Strand Alignment
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Bismark | 0.24.2 |